In the end it is revealed that John Shooter (Turturro) is actually a personality of a schizophrenic Mort Rainey (Depp). In the end, Shooter overwhelmed him, becoming the dominant personality, essentially destroying Mort. It is clear that Shooter pushed Rainey to correct his life, not the story, to take his revenge and kill his wife, Amy (Bello), whom he was currently going through a divorce with. After being confronted, Shooter took control of Rainey's body as Mort Rainey was unable to live with what Shooter had done on his behalf and performed a sort of 'mental suicide', as was hinted to by Shooter (now played by Depp) with the comment of "Now I never put a hand on him, Misses, I swear, he took the coward's way out." A fight ensued between the two, ending with Amy laying behind the house in the garden, wounded, unable to flee. Ted (Hutton) arrives, lured behind the house by Amy's screams. Shooter (Depp) kills both Amy and Ted with a shovel. Before he kills Amy, as he advances upon her, he recites the true ending of "Secret Window", the one he wanted Mort Rainey to replace with the 'ruined ending' Mort wrote."I know I can do it,' Todd Downey said, helping himself to another ear of corn from the steaming bowl. 'I'm sure that in time, every bit of her will be gone, and her death will be a mystery, even to me." He goes into town to shop, where the locals become unnerved by his presence, either tensing up or fleeing from the store. Later the Sheriff arrives at "Rainey's" cabin, discovering masses of corn in the kitchen. Rainey/Shooter is upstairs at the desk, now speaking in a confident manner, void of his Mississippi accent. The Sheriff tells 'Rainey' to stay out of town, they know what he did and that as soon as they found the bodies they could tie it to him. Rainey/Shooter agrees to shop out of town, grinning at the Sheriff as he states that the ending is the only thing that matters "This one's very good, this one's perfect." The last scenes are a tightly packed row of corns, growing in Amy's garden, now Amy and Ted's grave site, and Shooter/Rainey biting into an ear of corn.

In the opening scene, Mort closes the door of his jeep before he goes into the hotel room. You can hear the sound of the door closing and it's visible in the rearview-mirror. As the camera moves out of the room, the jeep door is completely open.